Digital Commons Network^™

Epidemiology Of Aspergillosis Diagnoses In Us Adults Using A National Ehr Database, 2013-2023., Brittany L. Morgan Bustamante, Elijah G. Martinez, Aidan Lee, Natalie J. Kane, Simon K. Camponuri, Rose M. Reynolds, Theo T. Snow, Juliana G E Bartels, Mark A. Hoffman, Theodore C. White, Justin V. Remais

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Aspergillosis is a fungal infection associated with rising hospitalizations and substantial morbidity and mortality. In the United States, data remain fragmented due to the absence of centralized surveillance. This study aimed to evaluate demographic, geographic, and temporal trends in aspergillosis diagnoses across the United States and evaluate changes in those patterns following the emergence of COVID-19.

METHODS: We conducted a retrospective cohort study using electronic health record data from 142 US healthcare systems (Oracle Health), including adults aged ≥18 years who received care between 2013 and 2023. The cohort included over 76 million patients and 127 million person-years. Aspergillosis …

Shiny-Magec: A Bayesian R Shiny Application For Meta-Analysis Of Censored Adverse Events, Zihan Zhou, Zizhong Tian, Christine Peterson, Le Bao, Shouhao Zhou

Faculty, Staff and Student Publications

Accurate assessment of adverse event (AE) incidence is critical in clinical research for drug safety. While meta-analysis serves as an essential tool to comprehensively synthesize the evidence across multiple studies, incomplete AE reporting in clinical trials remains a persistent challenge. In particular, AEs occurring below study-specific reporting thresholds are often omitted from publications, leading to left-censored data. Failure to account for these censored AE counts can result in biased AE incidence estimates. We present an R Shiny application that implements a Bayesian meta-analysis model specifically designed to incorporate censored AE data into the estimation process. This interactive tool provides a …

Linkage Disequilibrium Score Regression Identifies Genetic Correlations Between Hepatocellular Carcinoma And Clinically Relevant Traits, Younghun Han, Vikram R Shaw, Jinyoung Byun, Aaron P Thrift, Catherine Zhu, Donghui Li, Rikita I Hatia, Robin Kate Kelley, Sean P Cleary, Anna S Lok, Paige M Bracci, Jennifer B Permuth, Roxana Bucur, Jennifer Knox, Jian-Min Yuan, Amit G Singal, Prasun K Jalal, R Mark Ghobrial, Yuko Kono, Dimpy P Shah, Mindie H Nguyen, Neehar D Parikh, Richard Kim, Hui-Chen Wu, Hashem El-Serag, Ping Chang, Yun Shin Chun, Jian Gu, Chad Huff, Asif Rashid, Lu-Yu Hwang, Alison P Klein, Saira A Khaderi, Ahmed O Kaseb, Kathrine A Mcglynn, Lewis R Roberts, Manal M Hassan, Christopher I Amos

Faculty, Staff and Students Publications

Hepatocellular carcinoma (HCC) mortality is increasing globally, partly due to the growing prevalence of nonviral liver diseases. Genome-wide association studies (GWAS) have identified genetic variants associated with HCC development. Leveraging GWAS summary statistics and linkage disequilibrium score regression (LDSR), we investigated disease co-development with hepatitis C virus-negative (HCV-negative) HCC to provide unique insights into HCC etiology and prioritize relationships for further causal inquiry. We utilized the LDSR statistical framework to estimate the genetic correlation and heritability between HCV-negative HCC with 901 epidemiologic, behavioral, and clinical traits from the United Kingdom Biobank (UKBB). First, we set the threshold for observed scale …

The Role Of Top-Down Appetite Self-Regulation In The Development Of Healthy Eating Behaviors Among Children: A Narrative Review And Socialization Framework, David J Bridgett, Sheryl O Hughes, Matthew Broussard, Daniela Mccourt, Christina M Croce, Jennifer O Fisher

Faculty, Staff and Students Publications

Appetite self-regulation (ASR) among children is thought to have a fundamental role in shaping the development of healthy eating behaviors, dietary intake, and growth during childhood. Parallel to developmental frameworks for understanding "general" self-regulation among children, ASR has been described as involving children's use of "top-down" cognitive processes to moderate "bottom-up" biological drives around food approach and avoidance in the interest of achieving desired eating behaviors or outcomes. Whereas bottom-up ASR processes during early childhood are well characterized, particularly in the context of dysregulation and obesity risk, the role of top-down ASR processes in the development of healthy eating behaviors …

A Narrative Study On The Resilience Of Women In Technology Careers, Gina J. Baldridge

Electronic Theses and Dissertations

In spite of the promotion of science, technology, engineering, and mathematics (STEM) education and careers, there is a lack of women entering the STEM workforce and majoring in STEM subjects. Women can experience gender bias and workplace marginalization in STEM careers, but have learned coping strategies that have contributed to their technology career resilience. The purpose of this narrative qualitative study was to explore how women working as individual performers and leaders in technology companies told their career stories of resilience through the perspective of change acceptance, confidence, and communication, three factors in Kumar’s CR8 model of resilience. The model …

A Manifesto For Plant Science Education, Elizabeth Alvey, Andrea Paterlini, Mary E. Williams, Mia E. Cerfonteyn, Samantha Dobbie, Steven Dodsworth, Sonja D. Dunbar, Lauren R. Headland, Anastasia Kolesnikova, Pankaj Kumar, Silvia Manrique, Catherine Mansfield, Sebastian Stroud, Shannon Woodhouse, Hailey Ashton, Yoselin Benitez-Alfonso, Emily Breeze, Kelsey J.R.P. Byers, Chana P. Chetariya, Beth C. Dyson, Alec Forsyth, Beatriz Gonçalves, Camila Gonzalez, Daniel M. Jenkins, Joanna Kacprzyk, Kirsten Knox, George R. Littlejohn, Sara Lopez-Gomollon, Enrique López-Juez, Claudia Martinho

School of Biological and Marine Sciences

Societal Impact Statement: Plants provide oxygen, food, shelter, medicines and environmental services, without which human society could not exist. Tackling pressing and global challenges requires well-trained plant scientists and plant-aware individuals. This manifesto provides a practical evidence-based vision to strengthen plant science education, focused on five strategic priorities. It is relevant to all stakeholders within plant science and beyond: from frontline educators to institutional leaders; from commercial or charitable professionals to entrepreneurs and donors; from individual community members to their legislative representatives. Strengthening plant science education demands concrete actions from all stakeholders, ultimately to the benefit of us all. Summary: …

Systematic, Bibliographic And Statistical Aspects On Multi Generation Recycled Concrete Materials Research: A Review, Henrique Comba Gomes, Maozhou Meng, Katie Jones, William Vevers, Aissa Bouaissi, Boksun Kim

School of Engineering, Computing and Mathematics

This article aimed to review the current literature related to the topic of multiple generation recycled concrete materials considering systematic, bibliographic and statistical aspects. The review was conducted from an adaptation from the systematic review for engineering and experiments (SREE) method. Papers wrote in English with scientific relevance, title and abstract full aligned with the topic were selected from Scopus and Web of Science databases. Bibliographic aspects highlighted the research novelty, the quality of research and prominence for future works. The systematic review aimed to provide insights in the literature concerning multiple recycling concrete materials. Some of the main aspects …

Frontotemporal Network Interactions Causally Support Rapid Concreteness Judgments During Reading, Elliot Murphy, Oscar Woolnough, Cale W Morse, Xavier Scherschligt, Nitin Tandon

Faculty, Staff and Student Publications

Neurobiological models of conceptual processing have been limited in spatiotemporal resolution, and uncertainty remains about the causal role of specific regions in concept representation. We utilized intracranial recordings in human neurosurgical patients with epilepsy (n = 19) during a concreteness judgement paradigm of single word reading. Concrete concepts showed greater high-frequency activation across a frontal and ventrotemporal network, while greater activation for abstract words was found in lateral posterior middle temporal cortex. Intercortical communications, measured by high-frequency partial direct coherence, revealed bidirectional frontal and ventral plus lateral temporal interactions. Words occupying the middle range of the concreteness scale (e.g., "profit") …

Large Language Models For Bioinformatics, Wei Ruan, Yanjun Lyu, Jing Zhang, Jiazhang Cai, Peng Shu, Yang Ge, Yao Lu, Shang Gao, Yue Wang, Peilong Wang, Lin Zhao, Tao Wang, Yufang Liu, Luyang Fang, Ziyu Liu, Zhengliang Liu, Yiwei Li, Zihao Wu, Junhao Chen, Hanqi Jiang, Yi Pan, Zhenyuan Yang, Jingyuan Chen, Shizhe Liang, Wei Zhang, Terry Ma, Yuan Dou, Jianli Zhang, Xinyu Gong, Qi Gan, Yusong Zou, Zebang Chen, Yuanxin Qian, Shuo Yu, Jin Lu, Kenan Song, Xianqiao Wang, Andrea Sikora, Gang Li, Xiang Li, Quanzheng Li, Yingfeng Wang, Lu Zhang, Yohannes Abate, Lifang He, Wenxuan Zhong, Rongjie Liu, Chao Huang, Wei Liu, Ye Shen, Ping Ma, Hongtu Zhu, Yajun Yan, Dajiang Zhu, Tianming Liu

Faculty, Staff and Student Publications

With the rapid advancements in large language model technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and …

Tuscan: Tumor Segmentation And Classification Analysis In Spatial Transcriptomics, Chenxuan Zang, Charles C Guo, Yaohong Wang, Peng Wei, Ziyi Li

Faculty, Staff and Student Publications

The identification of tumor cells is pivotal for understanding tumor heterogeneity and the tumor microenvironment. Recent advances in spatially resolved transcriptomics (SRT) have revolutionized the way that transcriptomic profiles are characterized and have enabled the simultaneous quantification of transcript locations in intact tissue samples. SRT is a promising alternative method to study gene expression patterns in spatial domains. Nevertheless, the precise detection of tumor regions within intact tissue remains a great challenge. A common strategy for identifying tumor cells is via tumor-specific marker gene expression signatures, which are highly dependent on marker accuracy. Another effective approach is through aneuploid copy …

Severe Renal Phenotype Across A Multigenerational Tuberous Sclerosis Complex (Tsc) Family, Elena Tuller, Joshua A Samuels, Hope Northrup, Kate Richardson

Faculty, Staff and Student Publications

Background: Tuberous sclerosis complex (TSC) is an autosomal dominant genetic disorder characterized by the formation of hamartomas in the brain, kidney, and heart, along with other complex clinical manifestations, including TSC-associated neuropsychiatric disorder (TAND). Development of genotype-phenotype correlations within TSC can aid clinicians in providing prognostic data and improve clinical management. We present here a multigenerational family who has a pathogenic variant in TSC2 displaying a severe renal phenotype.

Methods: A 23-year-old Caucasian male (Patient 1) was determined to have a molecularly confirmed diagnosis of TSC at approximately 2 months of age. The nonsense pathogenic variant (c.1372C>T (p.Arg458*)) in …

Molecular And Regional Characterization Of Colorectal Polyps: Insights From Proteomics, Phosphoproteomics, And Immune Profiling., Thomas M. Attard, Shawn D. St Peter, Alexander Kats, Doug R. Lagemann, Caitlin E. Lawson, Badal C. Roy, Kafayat Yusuf, Lisa Harvey, Payel Bhanja, Rishi Man Chugh, Subhrajit Saha, Michael P. Washburn, Shahid Umar

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Familial adenomatous polyposis (FAP) is an inherited predisposition to colorectal cancer and characterized by profuse colorectal adenomas starting from the second decade of life. Regional (left vs. right) differences in the colonic microbiologic and immunologic microenvironment may impact adenoma evolution but are poorly understood. We aimed to characterize regional molecular, microbial, DNA damage, and immune differences in pediatric FAP polyps to test the hypothesis that polyps in pediatric FAP exhibit distinct regional and molecular features that contribute to differential growth and genomic instability.

METHODS: Colonic polyps and adjacent non-polyp mucosa were harvested from pediatric FAP patients undergoing colonoscopy. Tandem …

Mermaids In Pools: Ex-Situ Conservation As A Cornerstone For Sirenian Management Worldwide, D. N. Castelblanco-Martínez, E. A. Ramos, A. Alvarez-Alemán, F. L. N. Attademo, L. J. Cabrias-Contreras, D. Caicedo-Herrera, S. S. Landeo-Yauri, F. O. Luna, Miriam Marmontel, J. Sanchez, Carlos J. Silva, Vera Da Silva, Diogo Londero Da Silva, A. A. Mignucci-Giannoni

Faculty Publications

No abstract provided.

Evaluation Of Sanafoam Vaporooter Ii Stress On Activated Sludge Performance For Carbonaceous Removal And Nitrification, Ensiyeh Taheri, Ali Fatehizadeh, John Nazimek, Mustafa Nabi, Wayne Bagg, Amir Razmjou, Paul Nolan, Ratish Permala, Mehdi Khiadani

Research outputs 2022 to 2026

Root intrusion control in sewer pipelines often relies on chemical herbicides, yet their unintended impacts on downstream biological treatment remain underexplored. This study investigated the effects of Sanafoam Vaporooter II (SVII) on carbon removal and nitrification in activated sludge reactors (ASRs) under long-term operation. Two parallel bench-scale ASRs were installed and operated at Subiaco municipal wastewater treatment plant in Perth, Western Australia: one was exposed to incremental SVII concentrations (1–3000 mg/L), while the other served as an unamended control. Stoichiometric analysis revealed stable organic matter removal across all SVII doses. In contrast, nitrification decreased progressively at concentrations exceeding 128 mg/L. …

Comparison Of Analytical Techniques From The Extraction Of Bioactive Compounds From Kratom, Curry, Ginger, And Turmeric, Riley Bruno

Honors Program: Senior Projects (Public)

Plants, herbs, and spices have been used as medicines for thousands of years. Early civilizations often attributed healing properties of plants to magical or divine forces. However, as chemistry and analytical technology advanced between the 16th and 18th centuries, scientists began to understand that bioactive compounds within the plants actually caused these effects. Today, natural products remain extremely important in drug discovery. As the number of newly developed synthetic drugs declines, there has been renewed interest in identifying biologically active molecules from plants. Bioactive molecules are a group of diverse chemical compounds that stimulate a response in living tissues. The …

"Not A Textbook, But... ": Political Theory And The Biblical Narrative, Richard Mouw

Pro Rege

No abstract provided.

Jaundease Phototherapy Vest Test Plan, Sujay Panthulu, Jasdev Banwait, Gwynn Moss, Solomon M. Fernandez

Biomedical Engineering

Neonatal hyperbilirubinemia is a common condition affecting more than 60% of newborns, caused by an excess buildup of bilirubin in the blood due to the liver’s limited ability to process it efficiently [1]. The standard treatment involves hospital-based phototherapy, where infants are placed in incubators under blue light to break down bilirubin in the skin. Although effective, this approach requires infants to remain under the lights for 12–18 hours per day, often with eye protection, and separated from their parents—disrupting early bonding and potentially contributing to toxic stress that can impact neurological and emotional development [2]. While at-home phototherapy solutions …

Improving Cellular Retention And Distribution To Promote Arteriogenesis In A Mouse Model Of Chronic Arterial Occlusion, Nancy Huang

Biomedical Engineering

Peripheral Arterial Occlusive Disease (PAOD) affects millions of people in the United States, creating pain, discomfort, and limited mobility due to restricted blood flow from obstructed arteries. While current treatments include lifestyle changes and revascularization procedures, these options are often insufficient or inaccessible because of procedural pain and socioeconomic barriers. In some cases, this can lead to critical limb ischemia and amputation as a last resort. Increasing blood flow to the extremities by enhancing collateral vessel growth, a biological process called arteriogenesis, with cell-based therapies can redirect blood flow around obstructions and has potential to mitigate and treat the effects …

Iud Insertion Pain Management, Sandhya Sridhar, Olivia Armas, Lucy Campochiaro

Biomedical Engineering

This project focuses on developing an atraumatic cervical stabilization device that serves as a modern alternative to the traditional tenaculum used during IUD insertion procedures. Current devices rely on sharp metal prongs that pierce the cervix and often cause significant pain and bleeding. The goal of this project is to design a device that provides the same stability and control for clinicians while eliminating the need to puncture cervical tissue. The device is intended to be used by gynecologists, nurse practitioners, physician assistants, primary care physicians, or any medical professional performing an IUD insertion. The device is intended to be …

Orthopedic Bone Drill, Logan G. Schmid, Matthew T. Wold, May Geng

Biomedical Engineering

This project aims to design a bone drill for orthopedic procedures which alleviates the heat generated in the bone during drilling.

An Intersectional Framework For Effectively Mentoring Latinas In Stem Fields, Rosalynn A. Vega

Anthropology Faculty Publications

While Latinas are underrepresented across all areas of academia, this problem is especially severe in the science, technology, engineering, and mathematics (STEM) fields. This chapter offers a “best practices,” step‑by-step guide for how to effectively mentor Latinas in STEM fields—drawing from interdisciplinary concepts, culled from critical race studies, statistics, and anthropology—and personal experience as a Latina in STEM, mentor, and mentee. Crenshaw’s (1989) theory of intersectionality, Farmer’s (1999) notion of structural violence, and multivariate statistical modeling is used to demonstrate that intersectional inequality can be traced back to social structures. Multi‑gender and multiethnic mentoring by individuals who are motivated to …

Adapting Lessons From The Indian Subcontinent To Accelerate Elimination Of Visceral Leishmaniasis As A Public Health Problem In East Africa, Eva Iniguez, Daniel Masiga, Caryn Bern, Sridhar Srikantiah

All Peer-Reviewed Publications

This viewpoint draws lessons from the elimination of visceral leishmaniasis (VL) as a public health problem in the Southeast Asia region (SEAR) to inform efforts in East Africa (EA), now the global epicenter of Leishmania donovani transmission. VL is fatal and there is no licensed vaccine. Success in India relied on robust surveillance, rapid diagnosis, single-dose treatment, vector control, and multi-partner coordination. EA faces additional challenges than SEAR with multiple sand fly vectors, sensitive diagnostics and longer treatment regimens, high population mobility, and gaps in ecological and epidemiological knowledge. We highlight how strategies from South Asia could be adapted while …

An Adp Getaway Service, Not An Atp Tank: Insights Into The Phosphagen System In Neurons, Madeline P Marques, Kartik Venkatachalam

Faculty, Staff and Student Publications

No abstract provided.

Segmental Tracheal Resection For Thyroid Cancer: Perioperative Morbidity, Locoregional Control, And Survival, Anastasios Maniakas, David C Wilde, Isabelle Fournier, Emily K Hyde, Li Xu, Jennifer R Wang, Neil D Gross, Erich M Sturgis, Victoria Banuchi, Naifa L Busaidy, Maria E Cabanillas, Priyanka Iyer, Ramona Dadu, Steven G Waguespack, Mimi I Hu, G Brandon Gunn, Michael Kwon, Salmaan Ahmed, Michelle D Williams, Mark E Zafereo

Faculty, Staff and Student Publications

Background: Segmental tracheal resection is rarely needed for advanced thyroid cancer but is among the most complex, high-risk thyroid surgeries.

Methods: Retrospective study of patients undergoing segmental tracheal resection for thyroid cancer at MD Anderson Cancer Center (2005-2024).

Results: We identified 120 patients with a median follow-up of 4.6 years (range 0.02-16.38). Papillary thyroid cancer was most common (68%). The median number of tracheal rings resected was 4 (range 1-9). Seventeen (14%) patients had a new tracheostomy placed at the time of surgery, with 11 (9%) remaining trach-dependent at last follow-up. Twenty-six (22%) patients had a return to the operating …

Terraforming The Kras Lipid Landscape, Yong Zhou, John F Hancock

Faculty, Staff and Student Publications

No abstract provided.

Expanding Public Health Insurance To Parents: Effect On Parents' And Children’S Well-Being, Michelle Marcus, Xuan Zhang

Research Collection School Of Economics

Expanding public health insurance to parents may not only improve parental outcomes but also have spillover effects on their children. This paper leverages the natural experiment of the Affordable Care Act (ACA) to estimate the causal effects of expanding public health insurance to low-income parents on their well-being and that of their children. Using a difference-in-differences model and data from the 2010–2017 National Health Interview Surveys, we observe significant improvements in health care access, increased health care utilization, reduced financial burdens, and slight improvements in health status among low-income parents. For children in Medicaid expansion states, we find reductions in …

Unacceptable In Any Era: The Unusual And Unconstitutional Effort To Criminalize Sleeping While Homeless, Joseph W. Mead, Shelby Calambokidis

William & Mary Law Review

Grants Pass, Oregon, effectively made it a crime for some of its homeless residents to sleep—a universal and unavoidable biological necessity. In a 2024 decision, the Supreme Court held that the Eighth Amendment’s Cruel and Unusual Punishments Clause posed no obstacle to this law, but it emphasized that other constitutional provisions could place important limits on how cities treat their homeless residents.

This Article argues that modern laws criminalizing sleeping— especially when no shelter is available—represent an unprecedented and unconstitutional departure from centuries of American legal tradition. Tracing the evolution of vagrancy, poor relief, and settlement laws from the Statute …

Molecular Lung Imaging Following Exposure To Radiation Predicts Long-Term Survival In Rats, Anne V. Clough, Kathrina Mpala, Taheri Pardis, Laura Norwood Toro, Andreas M. Beyer, Tracy Gasperetti, Ming Zhao, Sarah Kerns, Heather A. Himburg, Said H. Audi

Mathematical and Statistical Science Faculty Research and Publications

Delayed effects of acute radiation exposure (DEARE), including radiation pneumonitis (lung-DEARE), develop weeks to months after radiation exposure. Pathway-targeted biomarkers that capture early oxidative stress and cell death could improve risk stratification and provide objective measures of mitigator efficacy. The objective was to test whether molecular lung imaging predicts long-term survival and mitigator response after irradiation. Rats received 13.5 Gy leg-out partial-body irradiation with a subset treated with the radiation-injury mitigator lisinopril. Rats underwent lung imaging at weeks 2 and 4 post-irradiation with ^99mTc-duramycin (cell death) and ^99mTc-HMPAO (oxidative stress). Plasma mitochondrial damage-associated molecular patterns (mtDAMPs) were also …

A Study Of Awareness Of Antiseptics And Disinfectant Use Among Allied Health Sciences Students And Interns Of A Tertiary Care Hospital, Pooja M, Puneeth A, Sharmi Nm

Digital Journal of Clinical Medicine

Background:

Antiseptics and disinfectants are among the most vital tools in infection prevention and control (IPC), especially in healthcare settings where the risk of hospital-acquired infections (HAIs) remains a significant concern. This study aims to assess the awareness and knowledge of antiseptics and disinfectants among Allied Health Sciences (AHS) students and interns, identify knowledge gaps at different stages of training, and recommend educational interventions.

Methods:

This was a cross-sectional, questionnaire-based study conducted among 1st to 3rd-year AHS students and interns at a tertiary care hospital. Data were collected using a validated questionnaire via a Google form after obtaining approval from …

Pseudo-Hallucinations: A Diagnostic Conundrum, Dr Sankram Nayak, Manju Aswath, Vathsalya S. Gowda

Digital Journal of Clinical Medicine

Background:

Pseudohallucinations are vivid, hallucination-like experiences that are internal, recognized as unreal. Distinguishing from true hallucinations remains a diagnostic challenge.

Case-report

33-year-old female with family history of psychosis presented with 10-year duration of delusion of infidelity and auditory experiences, with normal Biopsychosocial functioning. She had multiple psychiatric consultations, diagnosed as paranoid schizophrenia, treated with  various antipsychotics, ECT, current prescription of clozapine(350mg) with clozapine induced seizure.  Reported that her husband was emotionally unavailable. She described the voices in her head which were non-threatening, praising her for having qualities of an ideal-wife.  They were constant companions giving her solace and hence refrained …